<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">

<html lang="en">

<head>
  <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
  <title>LCOV - cover.info - /home/andres/Programacion/aso_coverage/aso/src/ASO/framework/therapy_gen_imp.cpp</title>
  <link rel="stylesheet" type="text/css" href="../../../../../../../../gcov.css">
</head>

<body>

  <table width="100%" border=0 cellspacing=0 cellpadding=0>
    <tr><td class="title">LCOV - code coverage report</td></tr>
    <tr><td class="ruler"><img src="../../../../../../../../glass.png" width=3 height=3 alt=""></td></tr>

    <tr>
      <td width="100%">
        <table cellpadding=1 border=0 width="100%">
        <tr>
          <td width="5%"></td>
          <td width="10%" class="headerItem">Current view:</td>
          <td width="35%" class="headerValue"><a href="../../../../../../../../index.html">directory</a> - <a href="index.html">home/andres/Programacion/aso_coverage/aso/src/ASO/framework</a> - therapy_gen_imp.cpp (source / <a href="therapy_gen_imp.cpp.func.html">functions</a>)</td>
          <td width="10%"></td>
          <td width="10%" class="headerCovTableHead">Found</td>
          <td width="10%" class="headerCovTableHead">Hit</td>
          <td width="15%" class="headerCovTableHead">Coverage</td>
          <td width="5%"></td>
        </tr>
        <tr>
          <td></td>
          <td class="headerItem">Test:</td>
          <td class="headerValue">cover.info</td>
          <td class="headerItem">Lines:</td>
          <td class="headerCovTableEntry">51</td>
          <td class="headerCovTableEntry">46</td>
          <td class="headerCovTableEntryHi">90.2 %</td>
        </tr>
        <tr>
          <td></td>
          <td class="headerItem">Date:</td>
          <td class="headerValue">2010-08-03</td>
          <td class="headerItem">Functions:</td>
          <td class="headerCovTableEntry">8</td>
          <td class="headerCovTableEntry">6</td>
          <td class="headerCovTableEntryMed">75.0 %</td>
        </tr>
                <tr><td><img src="../../../../../../../../glass.png" width=3 height=3 alt=""></td></tr>
        </table>
      </td>
    </tr>
    <tr><td class="ruler"><img src="../../../../../../../../glass.png" width=3 height=3 alt=""></td></tr>
  </table>

  <table cellpadding=0 cellspacing=0 border=0>
    <tr>
      <td><br></td>
    </tr>
    <tr>
      <td><pre class="source">
<a name="1"><span class="lineNum">       1 </span>                : /**</a>
<span class="lineNum">       2 </span>                :  * \file  therapy_gen_imp.cpp
<span class="lineNum">       3 </span>                :  * \brief implementation of TherapyGenImpl class.
<span class="lineNum">       4 </span>                :  *
<span class="lineNum">       5 </span>                :  * ASO: Antiviral Sequence Optimizer
<span class="lineNum">       6 </span>                :  * &lt;http://aso.googlecode.com/&gt;
<span class="lineNum">       7 </span>                :  * Copyright (C) 2010 Velez Ezequiel, Peralta Andres, FuDePAN
<span class="lineNum">       8 </span>                :  *
<span class="lineNum">       9 </span>                :  * This file is part of the ASO project.
<span class="lineNum">      10 </span>                :  *
<span class="lineNum">      11 </span>                :  * Contents:      CPP file for ASO providing class TherapyGenImpl.
<span class="lineNum">      12 </span>                :  *
<span class="lineNum">      13 </span>                :  * System:         ASO
<span class="lineNum">      14 </span>                :  * Language:       C++
<span class="lineNum">      15 </span>                :  *
<span class="lineNum">      16 </span>                :  * Author:         Velez Ezequiel, Peralta Andres
<span class="lineNum">      17 </span>                :  * E-Mail:
<span class="lineNum">      18 </span>                :  *
<span class="lineNum">      19 </span>                :  * ASO is free software: you can redistribute it and/or modify
<span class="lineNum">      20 </span>                :  * it under the terms of the GNU General Public License as published by
<span class="lineNum">      21 </span>                :  * the Free Software Foundation, either version 3 of the License, or
<span class="lineNum">      22 </span>                :  * (at your option) any later version.
<span class="lineNum">      23 </span>                :  *
<span class="lineNum">      24 </span>                :  * ASO is distributed in the hope that it will be useful,
<span class="lineNum">      25 </span>                :  * but WITHOUT ANY WARRANTY; without even the implied warranty of
<span class="lineNum">      26 </span>                :  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
<span class="lineNum">      27 </span>                :  * GNU General Public License for more details.
<span class="lineNum">      28 </span>                :  *
<span class="lineNum">      29 </span>                :  * You should have received a copy of the GNU General Public License
<span class="lineNum">      30 </span>                :  * along with ASO.  If not, see &lt;http://www.gnu.org/licenses/&gt;.
<span class="lineNum">      31 </span>                :  *
<span class="lineNum">      32 </span>                :  */
<span class="lineNum">      33 </span>                : 
<span class="lineNum">      34 </span>                : #include &quot;therapy_gen_imp.h&quot;
<span class="lineNum">      35 </span>                : #define DEBUG
<span class="lineNum">      36 </span>                : 
<span class="lineNum">      37 </span>                : #ifdef DEBUG
<span class="lineNum">      38 </span>                : size_t cant = 0;
<span class="lineNum">      39 </span>                : #endif
<a name="40"><span class="lineNum">      40 </span>                : </a>
<span class="lineNum">      41 </span>                : /*! Implementación de observer de mutantes*/
<span class="lineNum">      42 </span><span class="lineCov">             24 : void TherapyGenImpl::update(const MutantObs* m)</span>
<span class="lineNum">      43 </span>                : {
<span class="lineNum">      44 </span><span class="lineCov">             24 :     CAutonomousIterator&lt;SequenceSet&gt; mit(m-&gt;sequences);</span>
<span class="lineNum">      45 </span><span class="lineCov">             24 :     std::cout &lt;&lt; &quot;               N de mutantes: &quot; &lt;&lt; (m-&gt;sequences).size() &lt;&lt; std::endl;</span>
<span class="lineNum">      46 </span><span class="lineCov">            442 :     while (!mit.end())</span>
<span class="lineNum">      47 </span>                :     {
<span class="lineNum">      48 </span><span class="lineCov">            394 :         ChildId pToChild = pluginInterface-&gt;create_node(*mit, m-&gt;parent, m-&gt;antivirals, m-&gt;distance, ++currentId);</span>
<span class="lineNum">      49 </span>                : #ifdef DEBUG
<span class="lineNum">      50 </span><span class="lineCov">            394 :         ++cant;</span>
<span class="lineNum">      51 </span>                : #endif
<span class="lineNum">      52 </span><span class="lineCov">            394 :         const TherapyStatus status = pToChild-&gt;continue_therapy();</span>
<span class="lineNum">      53 </span><span class="lineCov">            394 :         switch (status)</span>
<span class="lineNum">      54 </span>                :         {
<span class="lineNum">      55 </span>                :             case Last :
<span class="lineNum">      56 </span>                :             {
<span class="lineNum">      57 </span><span class="lineNoCov">              0 :                 rankerObs-&gt;update(new Therapy(pToChild));</span>
<span class="lineNum">      58 </span><span class="lineNoCov">              0 :                 discard_node(pToChild);</span>
<span class="lineNum">      59 </span><span class="lineNoCov">              0 :                 break;</span>
<span class="lineNum">      60 </span>                :             }
<span class="lineNum">      61 </span>                :             case Continue :
<span class="lineNum">      62 </span>                :             {
<span class="lineNum">      63 </span><span class="lineCov">            394 :                 rankerObs-&gt;update(new Therapy(pToChild));</span>
<span class="lineNum">      64 </span>                : 
<span class="lineNum">      65 </span><span class="lineCov">            394 :                 GenerationPolicy::CallbackAction action = generation-&gt;node_creation_callback(pToChild, pToChild-&gt;scoring());</span>
<span class="lineNum">      66 </span>                : 
<span class="lineNum">      67 </span><span class="lineCov">            394 :                 if (action == GenerationPolicy::ProcessChild)</span>
<span class="lineNum">      68 </span>                :                 {
<span class="lineNum">      69 </span><span class="lineNoCov">              0 :                     process_node(pToChild);</span>
<span class="lineNum">      70 </span>                :                 }
<span class="lineNum">      71 </span><span class="lineCov">            394 :                 else if (action == GenerationPolicy::DiscardAndContinueWithSibling)</span>
<span class="lineNum">      72 </span>                :                 {
<span class="lineNum">      73 </span><span class="lineCov">             44 :                     discard_node(pToChild);    </span>
<span class="lineNum">      74 </span>                :                 }
<span class="lineNum">      75 </span><span class="lineCov">            394 :                 break;</span>
<span class="lineNum">      76 </span>                :             }
<span class="lineNum">      77 </span>                :             case Discard :
<span class="lineNum">      78 </span>                :             {
<span class="lineNum">      79 </span><span class="lineNoCov">              0 :                 discard_node(pToChild);</span>
<span class="lineNum">      80 </span>                :                 break;
<span class="lineNum">      81 </span>                :             }
<span class="lineNum">      82 </span>                :         }
<span class="lineNum">      83 </span><span class="lineCov">            394 :         ++mit;</span>
<span class="lineNum">      84 </span>                :     }
<span class="lineNum">      85 </span><span class="lineCov">             24 :     delete m;</span>
<span class="lineNum">      86 </span><span class="lineCov">             24 : }</span>
<a name="87"><span class="lineNum">      87 </span>                : </a>
<span class="lineNum">      88 </span>                : /*! descarto el nodo *id */
<span class="lineNum">      89 </span><span class="lineCov">            357 : void TherapyGenImpl::discard_node(const ChildId&amp; id)</span>
<span class="lineNum">      90 </span>                : {
<span class="lineNum">      91 </span><span class="lineCov">            357 :     delete id;</span>
<span class="lineNum">      92 </span><span class="lineCov">            357 : }</span>
<a name="93"><span class="lineNum">      93 </span>                : </a>
<span class="lineNum">      94 </span>                : /*! procesa el nodo *id */
<span class="lineNum">      95 </span><span class="lineCov">            313 : Score TherapyGenImpl::process_node(const ChildId&amp; id)</span>
<span class="lineNum">      96 </span>                : {
<span class="lineNum">      97 </span>                :     AntiviralSelector aVSelect;
<span class="lineNum">      98 </span><span class="lineCov">            313 :     const NucSequence sequence = id-&gt;sequence;</span>
<span class="lineNum">      99 </span><span class="lineCov">            313 :     AntiviralSet avApply;</span>
<span class="lineNum">     100 </span><span class="lineCov">            313 :     const Score score = id-&gt;scoring();</span>
<span class="lineNum">     101 </span><span class="lineCov">            313 :         std::cout &lt;&lt; &quot;&lt;&gt; nodo procesado &quot; &lt;&lt; id-&gt;get_id() &lt;&lt; std::endl;    </span>
<span class="lineNum">     102 </span><span class="lineCov">            313 :     pluginInterface-&gt;get_distance_matrix(matrix);</span>
<span class="lineNum">     103 </span><span class="lineCov">            313 :     aVSelect.select_antivirals(antivirals, sequence, avApply);      // veo los que aplican</span>
<span class="lineNum">     104 </span>                :     
<span class="lineNum">     105 </span><span class="lineCov">            313 :     if (!avApply.antivirals.empty())</span>
<span class="lineNum">     106 </span>                :     {
<span class="lineNum">     107 </span><span class="lineCov">            313 :         CombinationStatus cStatus;</span>
<span class="lineNum">     108 </span><span class="lineCov">            313 :         CombinationObserverImp Obs(sequence, id, this);</span>
<span class="lineNum">     109 </span><span class="lineCov">            313 :         CombinatoryPolicy* combinatoryPolicy = NULL; </span>
<span class="lineNum">     110 </span>                : 
<span class="lineNum">     111 </span><span class="lineCov">            313 :         combinatoryPolicy = id-&gt;get_combination_policy();</span>
<span class="lineNum">     112 </span>                : 
<span class="lineNum">     113 </span><span class="lineCov">            916 :         do</span>
<span class="lineNum">     114 </span>                :         {
<span class="lineNum">     115 </span><span class="lineCov">            916 : std::cout &lt;&lt; &quot;uso: &quot; &lt;&lt; combinatoryPolicy-&gt;get_name()&lt;&lt; &quot; con &quot;&lt;&lt; avApply.antivirals.size() &lt;&lt; std::endl;</span>
<span class="lineNum">     116 </span><span class="lineCov">            916 :             combinatoryPolicy-&gt;combine(avApply.antivirals, &amp;Obs, cStatus); //busco las combinaciones</span>
<span class="lineNum">     117 </span><span class="lineCov">            916 :             if(cStatus.status == Error)</span>
<span class="lineNum">     118 </span><span class="lineCov">            603 :                 combinatoryPolicy = id-&gt;virologic_failure(cStatus);</span>
<span class="lineNum">     119 </span>                :         }
<span class="lineNum">     120 </span>                :         while (cStatus.status == Error &amp;&amp; combinatoryPolicy != NULL);
<span class="lineNum">     121 </span>                : 
<span class="lineNum">     122 </span><span class="lineCov">            313 :         generation-&gt;post_combinations_callback(this);</span>
<span class="lineNum">     123 </span><span class="lineCov">            313 :                 std::cout &lt;&lt; &quot;---------- &quot; &lt;&lt;  id-&gt;get_id() &lt;&lt; std::endl;</span>
<span class="lineNum">     124 </span>                :     }
<span class="lineNum">     125 </span><span class="lineCov">            313 :     discard_node(id);</span>
<span class="lineNum">     126 </span><span class="lineCov">            313 :     return score;</span>
<a name="127"><span class="lineNum">     127 </span>                : }</a>
<span class="lineNum">     128 </span>                : 
<span class="lineNum">     129 </span><span class="lineCov">              1 : void TherapyGenImpl::generateTherapies(const NucSequence&amp; initSequence)</span>
<span class="lineNum">     130 </span>                : {
<span class="lineNum">     131 </span><span class="lineCov">              1 :     TherapyNode* const root = pluginInterface-&gt;create_node(initSequence, NULL, AntiviralSet(), ZERO_DISTANCE, currentId);</span>
<span class="lineNum">     132 </span><span class="lineCov">              1 :     process_node(root);</span>
<span class="lineNum">     133 </span>                : #ifdef DEBUG
<a name="134"><span class="lineNum">     134 </span><span class="lineCov">              1 :     std::cerr &lt;&lt; &quot;&gt;&gt;&gt;&gt;&gt; &quot; &lt;&lt; cant &lt;&lt; std::endl;</span></a>
<span class="lineNum">     135 </span>                : #endif
<span class="lineNum">     136 </span><span class="lineCov">              4 : }</span>
</pre>
      </td>
    </tr>
  </table>
  <br>

  <table width="100%" border=0 cellspacing=0 cellpadding=0>
  <tr><td class="ruler"><img src="../../../../../../../../glass.png" width=3 height=3 alt=""></td></tr>
  <tr><td class="versionInfo">Generated by: <a href="http://ltp.sourceforge.net/coverage/lcov.php" target="_parent">LCOV version 1.7</a></td></tr>
  </table>
  <br>

</body>
</html>
